The Bioinformatics Shared Resource (BISR) was established in 2004 with a focus on developing relational database resources for the AECC research community as the essential foundation for the management of data from high-throughput technologies (especially microarrays), and for the integration of data from different sources. Since then, the BISR has established web-based clinical study databases, and has adapted to the management of data from evolving microarray platforms and applications;in particular, the NimbleGen custom microarray system. The BISR has also been integrated into the cancer biomedical informatics grid (caBIG) project and currently has three contracts from NCI for its contributions to this program. The BISR is closely linked with the Biostatistics Shared Resource and is designed to focus on data management and mining, leaving the responsibility for data analysis with the latter facility. However, the expertise of both groups has been used to develop AECC's high-throughput analytical capabilities along with software programs to analyze microarray data that work within the database environment and generate not only the final output but also intermediate analyses that are informative about data quality. These analytical approaches are developed and supervised by AECC biostatisticians, but implemented by the BISR staff, leveraging the strengths of both groups to meet the evolving major challenge of processing and analyzing high-throughput genomic, epigenomic and proteomic data from basic and translational applications as they emerge and expand at this Center. The BISR has developed a pilot clinical study database for the AECC Head and Neck Cancer Affinity Group that allows the integration of laboratory and clinical data from multiple sources and maintains HIPAA-compliance through the use of metadata repositories that can be extrapolated to other disease sites. A second component to the bioinformatics infrastructure is being developed to support pre-existing applications such as TransFac, microarray analysis software, batched Blat and Entrez analyses, and biological pathway analysis tools such as GenMAPP and PathwayAssist. The facility is currently staffed by 5.25 FTE consisting of three bioinformaticists who provide consultative support to AECC members along with two programmers, and a part-time staff member who serves as a systems administrator and database administrator.